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[24.0] Raise RequestParameterInvalidException if collection element has unknown extension #17985

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@mvdbeek mvdbeek commented Apr 15, 2024

These might be typos or the result of bugs as in
#17938.

Fixes https://sentry.galaxyproject.org/share/issue/0761c11cefad49edae20bedbb4a662d7/:


Exception caught while attempting to execute tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.1':

AttributeError: 'NoneType' object has no attribute 'matches_any'
  File "galaxy/tools/__init__.py", line 1968, in handle_single_execution
    rval = self.execute(
  File "galaxy/tools/__init__.py", line 2065, in execute
    return self.tool_action.execute(
  File "galaxy/tools/actions/__init__.py", line 418, in execute
    ) = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
  File "galaxy/tools/actions/__init__.py", line 352, in _collect_inputs
    inp_data, all_permissions = self._collect_input_datasets(
  File "galaxy/tools/actions/__init__.py", line 292, in _collect_input_datasets
    tool.visit_inputs(param_values, visitor)
  File "galaxy/tools/__init__.py", line 1792, in visit_inputs
    visit_input_values(self.inputs, values, callback)
  File "galaxy/tools/parameters/__init__.py", line 211, in visit_input_values
    visit_input_values(
  File "galaxy/tools/parameters/__init__.py", line 227, in visit_input_values
    callback_helper(
  File "galaxy/tools/parameters/__init__.py", line 162, in callback_helper
    new_value = callback(**args)
  File "galaxy/tools/actions/__init__.py", line 259, in visitor
    if not datatype.matches_any(input.formats):

into something more useful for users.

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

These might be typo's or the result of bugs as in
galaxyproject#17938.

Fixes:
```

Exception caught while attempting to execute tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.1':

AttributeError: 'NoneType' object has no attribute 'matches_any'
  File "galaxy/tools/__init__.py", line 1968, in handle_single_execution
    rval = self.execute(
  File "galaxy/tools/__init__.py", line 2065, in execute
    return self.tool_action.execute(
  File "galaxy/tools/actions/__init__.py", line 418, in execute
    ) = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info)
  File "galaxy/tools/actions/__init__.py", line 352, in _collect_inputs
    inp_data, all_permissions = self._collect_input_datasets(
  File "galaxy/tools/actions/__init__.py", line 292, in _collect_input_datasets
    tool.visit_inputs(param_values, visitor)
  File "galaxy/tools/__init__.py", line 1792, in visit_inputs
    visit_input_values(self.inputs, values, callback)
  File "galaxy/tools/parameters/__init__.py", line 211, in visit_input_values
    visit_input_values(
  File "galaxy/tools/parameters/__init__.py", line 227, in visit_input_values
    callback_helper(
  File "galaxy/tools/parameters/__init__.py", line 162, in callback_helper
    new_value = callback(**args)
  File "galaxy/tools/actions/__init__.py", line 259, in visitor
    if not datatype.matches_any(input.formats):
```

into something more useful for users.
@mvdbeek mvdbeek changed the title Raise MessagException if collection element has unknown extension [24.0] Raise MessagException if collection element has unknown extension Apr 15, 2024
@github-actions github-actions bot added this to the 24.1 milestone Apr 15, 2024
@mvdbeek mvdbeek merged commit 3c2db48 into galaxyproject:release_24.0 Apr 16, 2024
52 of 53 checks passed
@nsoranzo nsoranzo deleted the invalid_datatype_message_fix branch April 16, 2024 09:54
@nsoranzo nsoranzo changed the title [24.0] Raise MessagException if collection element has unknown extension [24.0] Raise RequestParameterInvalidException if collection element has unknown extension Apr 16, 2024
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